MBP Reader is actually a Perl script you can use directly on the Mac via Terminal, which is how I do it. The windows version is just a wrapper around it.

There is a warning that the latest Kindle updates seem to have changed the way that the notes are stored, so MBP Reader might no longer work for them.

The last time I used it was Aug. 23, and those files are perfect. I've just tested two .mbp files - one from my Kindle 3 (3.0.1) and another from my DXG (2.5.5) - only the number of marks was extracted, not the text. And it generated no errors. Grrr.